ODK-built AgrO

.github/ISSUE_TEMPLATE/README.md

@@ -45,24 +45,10 @@ Others:
 
 ---
 
-
 ## Issue forms upgrade
 
 Used github issue forms template for new issues.
 References:
 
 - [Github Community - Issue Template](https://gh-community.github.io/issue-template-feedback/structured/)
 - [Github Docs](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository#creating-issue-templates)
-
-## Fields
-**AgrO term**: 
-> ID and Label (ie. `[liming process](http://purl.obolibrary.org/obo/AGRO_00000112)`)
-
-**Suggested new label:**: 
-
-**_Optional_**: 
-> Any additional information (like supporting evidence, PubMed ID, etc.)
-
-**Your nano-attribution (ORCID)**: 
-> If you don't have an ORCID, you can sign up for one [here](https://orcid.org/)
-

.github/ISSUE_TEMPLATE/add-synonym.yml

@@ -1,4 +1,4 @@
-name: Add synonym
+name: Term - synonym add 
 description: New synonym suggestion for an existing AgrO term.
 title: '[Synonym] '
 labels: [term-annot]
@@ -20,7 +20,6 @@ body:
       description: ie, broad/exact/narrow/related
     validations:
       required: true
-
   - type: input
     id: subtype
     attributes:
@@ -36,7 +35,6 @@ body:
       description: Such as PURL, source (website) or a cross-reference to another ontology, like ENVO or PATO.
     validations:
       required: false
-
   - type: input
     id: attribution
     attributes:

.github/ISSUE_TEMPLATE/add-term.yml

@@ -1,16 +1,15 @@
-name: Add new term
+name: Term - add new 
 description: New term suggestion for AgrO
 title: "[NTR] "
 labels: [term-add]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term
     attributes:
-      label: AgrO term
-      description: ID and Label
-      placeholder: "[liming process](http://purl.obolibrary.org/obo/AGRO_00000112)"
+      label: Proposed term label
+      description: Please enter the label as found in a published source
+      placeholder: "liming process"
     validations:
       required: true
 
@@ -33,7 +32,7 @@ body:
     id: Parent
     attributes:
       label: Parent term
-      description: use [OLS](https://www.ebi.ac.uk/ols/ontologies/AgrO), or your favorite ontology browser
+      description: Please list term(s) which this term should be under? (Hint- [OLS](https://www.ebi.ac.uk/ols/ontologies/AgrO) allows east searching)
     validations:
       required: true
 

.github/ISSUE_TEMPLATE/typos-bugs-errors.yml → .github/ISSUE_TEMPLATE/bugs-errors.yml

@@ -1,8 +1,7 @@
-name: Typos/Bugs/Errors
-description: Report all kinds of typos or bugs in AgrO
+name: Bugs/Errors
+description: Report bugs/errors in AgrO
 labels: [bug]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/ISSUE_TEMPLATE/custom.yml

@@ -1,8 +1,20 @@
-name: Custom issue template
+name: Custom issue template (Feature Request/Help/Question)
 description: When the issue isn't defined by other templates. Please provide as many references to resources mentioned as timely available.
 assignees: krishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
+  - type: checkboxes
+    id: feature
+    attributes:
+      label: feature
+      description: "Please check if this issue involves the following:"
+      options:
+        - label: "Feature Request"
+        - label: "Help/Question on AgrO"
+
+  - type: markdown
+    attributes:
+      value: "Note: For bug reports, please switch to the Typos/Bugs/Errors issue template"
+
   - type: textarea
     id: desc
     attributes:

.github/ISSUE_TEMPLATE/fix-xref.yml

@@ -1,9 +1,8 @@
-name: Fix/Add xref (source link, ex. for definitions)
+name: Term - annotations fix/add xref (source link, ex. for definitions)
 description: Report issue about incorrect xref source on term.
 title: '[xRef] '
 labels: [term-annot]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/ISSUE_TEMPLATE/import-term.yml

@@ -0,0 +1,46 @@
+name: Term - import/transfer
+description: Import term from registered Ontology into AgrO
+title: "[Import] "
+labels: [term-add]
+assignees: KrishnaTO
+body:
+  - type: checkboxes
+    id: transfer
+    attributes:
+      label: Are you requesting to import or transfer the term?
+      description: "Importing a term makes a term local to AgrO and accessible offline. Transferring a term means the term has been previously published in other Ontology but is a better fit in AgrO (Ideally, only curators should be making this request)."
+      options:
+        - label: "Import term into AgrO from another Ontology"
+        - label: "Transfer term into AgrO from another Ontology"
+
+  - type: input
+    id: term
+    attributes:
+      label: Term label
+      description: Please list the label and IRI from the registered ontologies
+      placeholder: "[liming process](http://purl.obolibrary.org/obo/AGRO_00000112)"
+    validations:
+      required: true
+
+  - type: input
+    id: Parent
+    attributes:
+      label: Parent term
+      description: Please list term(s) which this term should be under? (Hint- [OLS](https://www.ebi.ac.uk/ols/ontologies/AgrO) allows east searching)
+    validations:
+      required: true
+
+  - type: textarea
+    id: reason
+    attributes:
+      label: Please state the reason to import the term into AgrO
+    validations:
+      required: false
+
+  - type: input
+    id: attribution
+    attributes:
+      label: Your nano-attribution (ORCID)
+      description: If you don't have an ORCID, you can sign up for one [here](https://orcid.org/)
+    validations:
+      required: false

.github/ISSUE_TEMPLATE/mergeTerm.yml

@@ -1,9 +1,8 @@
-name: Merge two terms
+name: Term - merge
 description: Merge with another AgrO term and obsolete/deprecate an existing AgrO term
 title: "[Merge] "
 labels: [term-mod]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/ISSUE_TEMPLATE/obsolete-a-term.yml

@@ -1,9 +1,8 @@
-name: Obsolete a term
+name: Term - obsolete
 description: Obsolete or deprecate an existing AgrO term
 title: "[Obsolete] "
 labels: [term-mod]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/ISSUE_TEMPLATE/qc.yml

@@ -2,7 +2,6 @@ name: Quality Control
 description: Quality Control issues, addressing automated reports (ie. ROBOT report) or workflows modifications/suggestions
 labels: [QC]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE) 
 body:
   - type: input
     id: report

.github/ISSUE_TEMPLATE/relabel-term.yml

@@ -1,9 +1,8 @@
-name: Relabel term
+name: Term - relabel
 description: Suggested revised label (IAO_0000115) for a AgrO term.
 title: '[Label] '
 labels: [term-annot]
 assignees: krishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/ISSUE_TEMPLATE/revise-logical-definition.yml

@@ -1,8 +1,7 @@
-name: Revise logical definition in subdomain
-description: Improve the OWL-DL statement of a AgrO term; issues involving terms in multiple ontologies, overclassified/overgeneralized subdomain terms (ie. subdomain= Fertilizer) 
+name: Description Logics (DL) revision of term
+description: Improve the OWL-DL statement (EquivalentTo, SubClassOf, etc) of a AgrO term
 labels: [term-logic]
 assignees: krishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/ISSUE_TEMPLATE/revise-textual-definition.yml

@@ -1,9 +1,8 @@
-name: Revise textual definition
+name: Term - definition revision
 description: Change the textual definition of an AgrO term
 title: "[Def] "
 labels: [term-annot]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/ISSUE_TEMPLATE/split-term.yml

@@ -1,9 +1,8 @@
-name: Split term
+name: Term - split
 description: Request to split a term into two or more terms
 title: '[Split] '
 labels: [term-add]
 assignees: KrishnaTO
-# Template originally forked from [@mondo](https://github.com/monarch-initiative/mondo/tree/master/.github/ISSUE_TEMPLATE)
 body:
   - type: input
     id: term

.github/workflows/qc.yml

@@ -0,0 +1,33 @@
+# Basic ODK workflow
+
+name: CI
+
+# Controls when the action will run. 
+on:
+  # Triggers the workflow on push or pull request events but only for the main branch
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "ontology_qc"
+  ontology_qc:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: obolibrary/odkfull:v1.2.32
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Run ontology QC checks
+        env:
+          DEFAULT_BRANCH: main
+        run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false
+

.gitignore

@@ -1,10 +1,39 @@
-src/ontology/mirror/bfo.owl
-src/ontology/mirror/chebi.owl
-src/ontology/mirror/envo.owl
-src/ontology/mirror/pato.owl
-src/ontology/mirror/iao.owl
-src/ontology/catalog-v001.xml
-src/ontology/catalog-v001.xml
+.DS_Store
+semantic.cache
+bin/
+
+*.tmp
+*.tmp.obo
+*.tmp.owl
+*.tmp.json
+
 src/ontology/mirror
 src/ontology/mirror/*
-src/ontology/envo-test/Makefile
+src/ontology/reports/*
+src/ontology/agro.owl
+src/ontology/agro.obo
+src/ontology/agro.json
+src/ontology/agro-base.*
+src/ontology/agro-basic.*
+src/ontology/agro-full.*
+src/ontology/agro-simple.*
+src/ontology/agro-simple-non-classified.*
+
+src/ontology/seed.txt
+src/ontology/dosdp-tools.log
+src/ontology/ed_definitions_merged.owl
+src/ontology/ontologyterms.txt
+src/ontology/simple_seed.txt
+src/ontology/patterns
+src/ontology/merged-agro-edit.owl
+
+src/ontology/target/
+src/ontology/tmp/*
+!src/ontology/tmp/README.md
+
+src/ontology/imports/*_terms_combined.txt
+
+src/patterns/data/**/*.ofn
+src/patterns/data/**/*.txt
+src/patterns/pattern_owl_seed.txt
+src/patterns/all_pattern_terms.txt

CONTRIBUTING.md

@@ -0,0 +1,15 @@
+## Before you write a new request, please consider the following: 
+
+- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, either as a primary term or a synonym term. You can search using [OLS](http://www.ebi.ac.uk/ols/ontologies/agro)
+
+## Guidelines for creating GitHub tickets with contributions to the ontology:
+
+1. **Write a detailed request:** Please be specific and include as many details as necessary, providing background information, and if possible, suggesting a solution. GOC editors will be better equipped to address your suggestions if you offer details regarding *'what is wrong'*, *'why'*, and *'how to fix it'*.
+
+2. **Provide examples and references:** Please include PMIDs for new term requests, and include also screenshots, or URLs illustrating the current ontology structure for other types of requests. 
+
+3. **For new term request:** Be sure to provide suggestions for label (name), definition, references, position in hierarchy, etc.
+
+4. **For updates to relationships:** Provide details of the current axioms, why you think they are wrong or not sufficient, and what exactly should be added or removed.
+
+On behalf of the Agronomy ontology editorial team, Thanks!